Understanding the Assembly Mechanism of Proteins from Monte Carlo Simulations

Full-Text HTML XML Download Download as PDF (Size:1199KB) PP. 280-292
DOI: 10.4236/am.2017.83023    375 Downloads   552 Views  

ABSTRACT

Understanding the molecular mechanism of the protein assembly still remains a challenge in the case of many biological systems. In this frame, the mechanism which drives RodA hydrophobins to self-assemble onto the surface of the conidia of the human fungal pathogen Aspergillus fumigatus into highly ordered nanorods known as rodlets, is still unresolved. Here, AFM investigations were combined with Monte Carlo simulations to elucidate how these small amphiphilic proteins self-assemble into tightly packed rodlets and how they are further organized in nanodomains. It becomes that the assembly of RodA hydrophobins into rodlets and their parallel alignment within nanodomains result from their anisotropic properties. Monte Carlo simulations allowed us to confirm that anisotropic interactions between macromolecules are sufficient to drive them to assembly into rodlets prior to nanodomains formation. Better knowledge of the mechanism of hydrophobins assembly into rodlets offers new prospects for the development of novel strategies leading to inhibition of rodlet formation, which should allow more rapid detection of the conidia by the immune system.

Cite this paper

Cuenot, S. , Zykwinska, A. , Radji, S. and Bouchara, J. (2017) Understanding the Assembly Mechanism of Proteins from Monte Carlo Simulations. Applied Mathematics, 8, 280-292. doi: 10.4236/am.2017.83023.

References

[1] Chiti, F. and Dobson, C.M. (2006) Protein Misfolding, Functional Amyloid, and Human Disease. Annual Review of Biochemistry, 75, 333-366.
https://doi.org/10.1146/annurev.biochem.75.101304.123901
[2] Uversky, V.N. and Eliezer, D. (2009) Biophysics of Parkinson’s Disease: Structure and Aggregation of α-Synuclein. Current Protein & Peptide Science, 10, 483-499.
https://doi.org/10.2174/138920309789351921
[3] Andersson, A., Bohman, S., Borg, L.A.H., Paulsson, J.F., Schultz, S.W., Westermark, G.T. and Westermark, P. (2008) Amyloid Deposition in Transplanted Human Pancreatic Islets: A Conceivable Cause of Their Long-Term Failure. Experimental Diabetes Research, 2008, Article ID: 562985.
https://doi.org/10.1155/2008/562985
[4] Auer, S., Dobson, C.M., Vendruscolo, M. and Maritan, A. (2008) Self-Templated Nucleation in Peptide and Protein Aggregation. Physical Review Letters, 101, Article ID: 258101.
https://doi.org/10.1103/physrevlett.101.258101
[5] Bianchi, E., Blaak, R. and Likos, C.N. (2011) Patchy Colloids: State of the Art and Perspectives. Physical Chemistry Chemical Physics, 13, 6397-6410.
https://doi.org/10.1039/c0cp02296a
[6] Doppelbauer, G., Bianchi, E. and Kahl, G. (2010) Self-Assembly Scenarios of Patchy Colloidal Particles in Two Dimensions. Journal of Physics: Condensed Matter, 22, Article ID: 104105.
https://doi.org/10.1088/0953-8984/22/10/104105
[7] Irback, A., Jonsson, S.A., Linnemann, N., Linse, B. and Wallin, S. (2013) Aggregate Geometry in Amyloid Fibril Nucleation. Physical Review Letters, 110, Article ID: 058101.
https://doi.org/10.1103/physrevlett.110.058101
[8] Latgé, J.P. (1999) Aspergillus fumigatus and Aspergillosis. Clinical Microbiology Reviews, 12, 310-350.
[9] Nivoix, Y., Velten, M., Letscher-Bru, V., Moghaddam, A., Natarajan-Amé, S., Fohrer, C., Lioure, B., Bilger, K., Lutun, P., Marcellin, L., Launoy, A., Bergerat, J.P. and Herbrecht, R. (2008) Factors Associated with Overall and Attributable Mortality in Invasive Aspergillosis. Clinical Infectious Diseases, 47, 1176-1184.
https://doi.org/10.1086/592255
[10] Tronchin, G., Pihet, M., Lopes-Bezerra, L.M. and Bouchara, J.-P. (2008) Adherence Mechanisms in Human Pathogenic Fungi. Medical Mycology, 46, 749-772.
https://doi.org/10.1080/13693780802206435
[11] Thau, N., Monod, M., Crestani, B., Rolland, C., Tronchin, G., Latgé, J.-P. and Paris, S. (1994) Rodletless Mutants of Aspergillus fumigates. Infection and Immunity, 62, 4380-4388.
[12] Paris, S., Debeaupuis, J.-P., Crameri, R., Carey, M., Charlès, F., Prévost, M.C., Schmitt, C., Philippe, B. and Latgé, J.-P. (2003) Conidial Hydrophobins of Aspergillus fumigatus. Applied and Environmental Microbiology, 69, 1581-1588.
https://doi.org/10.1128/AEM.69.3.1581-1588.2003
[13] Aimanianda, V., Bayry, J., Bozza, S., Kniemeyer, O., Perruccio, K., RamuluElluru, S., Clavaud, C., Paris, S., Brakhage, A.A., Kaveri, S.V., Romani, L. and Latgé, J.-P. (2009) Surface Hydrophobin Prevents Immune Recognition of Airborne Fungal Spores. Nature, 460, 1117-1121.
https://doi.org/10.1038/nature08264
[14] Dague, E., Alsteens, D., Latgé, J.-P., Verbelen, C., Raze, D., Baulard, A.R. and Dufrêne, Y.F. (2007) Chemical Force Microscopy of Single Live Cells. Nano Letters, 7, 3026-3030.
https://doi.org/10.1021/nl071476k
[15] Kwan, A.H., Winefield, R.D., Sunde, M., Matthews, J.M., Haverkamp, R.G., Templeton, M.D. and Mackay, J.P. (2006) Structural Basis for Rodlet Assembly in Fungal Hydrophobins. Proceedings of the National Academy of Sciences of the United States of America, 103, 3621-3626.
https://doi.org/10.1073/pnas.0505704103
[16] Kwan, A.H., Macindoe, I., Vukasin, P.V., Morris, V.M., Kass, I., Gupte, R., Mark, A.E., Templeton, M.D., Mackay, J.P. and Sunde, M. (2008) The Cys3-Cys4 Loop of the Hydrophobin EAS Is Not Required for the Formation and Surface Activity. Journal of Molecular Biology, 382, 708-720.
https://doi.org/10.1016/j.jmb.2008.07.034
[17] Macindoe, I., Kwan, A.H., Ren, Q., Morris, V.K., Yang, W., Mackay, J.P. and Sunde, M. (2012) Self-Assembly of Functional, Amphipathic Amyloid Monolayers by the Fungal Hydrophobin EAS. Proceedings of the National Academy of Sciences of the United States of America, 109, 804-811.
https://doi.org/10.1073/pnas.1114052109
[18] Nelson, R., Sawaya, M.R., Balbirnie, M., Madsen, A.O., Riekel, C., Grothe, R. and Eisenberg, D. (2005) Structure of the Cross-Beta Spine of Amyloid-Like Fibrils. Nature, 435, 773-778.
https://doi.org/10.1038/nature03680
[19] Goldschmidt, L., Teng, P.K., Riek, R. and Eisenberg, D. (2010) Identifying the Amylome, Proteins Capable of Forming Amyloid-Like Fibrils. Proceedings of the National Academy of Sciences of the United States of America, 107, 3487-3492.
https://doi.org/10.1073/pnas.0915166107
[20] Dague, E., Alsteens, D., Latgé, J.-P. and Dufrêne, Y.F. (2008) High-Resolution Cell Surface Dynamics of Germinating Aspergillus fumigatus Conidia. Biophysical Journal, 94, 656-660.
https://doi.org/10.1529/biophysj.107.116491
[21] Zykwinska, A., Pihet, M., Radji, S., Bouchara, J.-P. and Cuenot, S. (2014) Self-Assembly of Proteins into a Three-Dimensional Multilayer System: Investigation of the Surface of the Human Fungal Pathogen Aspergillus fumigatus. Biochimica et Biophysica Acta, 1844, 1137-1144.
https://doi.org/10.1016/j.bbapap.2014.03.001
[22] Wosten, H.A.B., Schuren, F.H.J. and Wessels, J.G.H. (1994) Interfacial Self-Assembly of a Hydrophobin into an Amphipathic Protein Membrane Mediates Fungal Attachment to Hydrophobic Surfaces. EMBO Journal, 13, 5848-5854.
[23] Gibbs, J.W. (1931) The Collected Works of J. W. Gibbs. Longmans, Green, New York, Vol. 1, 219.
[24] Adamson, A.W. and Gast, A.P. (1997) Physical Chemistry of Surfaces. 4th Edition, John Wiley, New York.
[25] Fung, S.Y., Keyes, C., Duhamel, J. and Chen, P. (2003) Concentration Effect on the Aggregation of a Self-Assembling Oligopeptide. Biophysical Journal, 85, 537-548.
https://doi.org/10.1016/S0006-3495(03)74498-1
[26] Liu, X.Y. (2000) Molecular Modelling for Non-Ideal Mixing of Amphiphilic Molecules. Langmuir, 18, 14-25.
https://doi.org/10.1021/la0105329
[27] Sipe, J.D. and Cohen, J.D. (2000) Review: History of the Amyloid Fibril. Journal of Structural Biology, 130, 88-98.
https://doi.org/10.1006/jsbi.2000.4221
[28] Wang, X., Graveland-Bikker, J.F., de Kruif, C.G. and Robillard, G.T. (2004) Oligomerization of Hydrophobin SC3 in Solution: From Soluble State to Self-Assembly. Protein Science, 13, 810-821.
https://doi.org/10.1110/ps.03367304
[29] Zykwinska, A., Guillemette, T., Bouchara, J.-P. and Cuenot, S. (2014) Spontaneous Self-Assembly of SC3 Hydrophobins into Nanorods in Aqueous Solution. Biochimica et Biophysica Acta, 1844, 1231-1237.
https://doi.org/10.1016/j.bbapap.2014.04.003
[30] Tavares, J.M., Holder, B. and Telo da Gama, M.M. (2009) Structure and Phase Diagram of Self-Assembled Rigid Rods: Equilibrium Polydispersity and Nematic Ordering in Two Dimensions. Physical Review E, 79, Article ID: 021505.
https://doi.org/10.1103/PhysRevE.79.021505
[31] Longone, P., Linares, D.H. and Ramirez-Pastor, A.J. (2010) Critical Behaviour of Attractive Rigid Rods on Two-Dimensional Lattices. Journal of Chemical Physics, 132, Article ID: 184701.
https://doi.org/10.1063/1.3424775
[32] Ghosh, A. and Dhar, D. (2007) On the Orientational Ordering of Long Rods on a Lattice. Europhysics Letters, 78, 20003.
https://doi.org/10.1209/0295-5075/78/20003
[33] Doye, J.P.K., Louis, A.A., Lin, I.-C., Allen, L.R., Noya, E.G., Wilber, A.W., Kok, H.C. and Lyus, R. (2007) Controlling Crystallization and Its Absence: Proteins, Colloids and Patchy Models. Physical Chemistry Chemical Physics, 9, 2197-2205.
https://doi.org/10.1039/b614955c
[34] Schwen, E.M., Mazilu, I. and Mazilu, D.A. (2015) A Stochastic Model of Particle Deposition and Evaporation for Ionic Self-Assembly of Thin Films. Journal of Physics, 574, Article ID: 012043.
https://doi.org/10.1088/1742-6596/574/1/012043

  
comments powered by Disqus

Copyright © 2017 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.